2JEC

crystal structure of recombinant DiocleA grandiflora lectin mutant E123A-H131N-K132Q complexed witH 5-bromo-4-chloro-3-indolyl-a-D- mannose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JE9PDB ENTRY 2JE9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 18% PEG 8000, 0.1M CACODYLATE, PH 6.5 AND 0.2M ZINC ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.6152.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.194α = 90
b = 84.552β = 90
c = 176.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1228.999.60.0712.93.8733522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111000.2533.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JE9288.0469591370299.50.1820.1790.23RANDOM19.04
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.060.61-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.168
r_dihedral_angle_4_deg13.407
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg7.742
r_angle_refined_deg1.508
r_nbtor_refined0.301
r_nbd_refined0.2
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.168
r_dihedral_angle_4_deg13.407
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg7.742
r_angle_refined_deg1.508
r_nbtor_refined0.301
r_nbd_refined0.2
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.16
r_chiral_restr0.104
r_metal_ion_refined0.085
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7223
Nucleic Acid Atoms
Solvent Atoms740
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing